SMTL ID : 4obh.2 (1 other biounit)

Crystal Structure of Inactive HIV-1 Protease in Complex with the p1-p6 substrate variant (L449F)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-1-mer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 2 residues within 4Å: Chain A: M.36, N.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.37

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: D.29, D.30, M.46 Chain C: R.1, G.3 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.1, C:R.1, A:D.29, A:D.30 Water bridges: C:G.3 EDO.3: 6 residues within 4Å: Chain A: T.12, R.14, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.65, A:E.65, A:G.68 EDO.4: 4 residues within 4Å: Chain A: K.20, E.21, E.34, N.83 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.21, A:E.34, A:E.34, A:N.83 Water bridges: A:E.34 EDO.7: 5 residues within 4Å: Chain B: I.72, G.73, T.74, N.88, Q.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.74, B:T.74, B:T.74, B:N.88, B:Q.92 EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: T.12, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.65, B:C.67, B:G.68 EDO.10: 4 residues within 4Å: Chain B: I.15, G.16, G.17, Q.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.17, B:Q.18

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.87 Chain B: K.7, R.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.87, A:R.87, B:R.8 Water bridges: B:R.8 GOL.6: 7 residues within 4Å: Chain A: L.5, W.6 Chain B: D.29, R.87, N.88 Chain C: R.9 Ligands: PO4.11 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:D.29, B:R.87, B:R.87, A:W.6, C:R.9

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 6 residues within 4Å: Chain A: W.6, K.7, R.8 Chain B: R.87 Chain C: R.9 Ligands: GOL.6 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Salt bridges: B:R.87, C:R.9 Hydrogen bonds: A:R.8, A:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolli, M. et al., HIV-1 protease-substrate coevolution in nelfinavir resistance. J.Virol. (2014)

Release Date

2014-11-26

Peptides

HIV-1 Protease: AB
p1-p6 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

HIV-1 Protease

p1-p6 peptide

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